From b78fb1a396fb5bcc5f6b428e6514061328464cde Mon Sep 17 00:00:00 2001
From: kjvdheide <kjvanderheide@dundee.ac.uk>
Date: Mon, 30 Oct 2017 15:33:41 +0000
Subject: [PATCH] JAL-2795 implemented getting/setting identifiers

---
 src/jalview/ext/forester/ForesterMatrix.java |   27 +++++++++++++++++++-------
 1 file changed, 20 insertions(+), 7 deletions(-)

diff --git a/src/jalview/ext/forester/ForesterMatrix.java b/src/jalview/ext/forester/ForesterMatrix.java
index daeec3b..cac1993 100644
--- a/src/jalview/ext/forester/ForesterMatrix.java
+++ b/src/jalview/ext/forester/ForesterMatrix.java
@@ -7,6 +7,7 @@ import java.io.IOException;
 import java.io.Writer;
 import java.text.DecimalFormat;
 import java.text.NumberFormat;
+import java.util.Arrays;
 
 import org.forester.evoinference.matrix.distance.DistanceMatrix;
 import org.forester.util.ForesterUtil;
@@ -29,11 +30,17 @@ public class ForesterMatrix implements DistanceMatrix
     this.jalviewMatrix = jalviewInputMatrix;
     this.sequences = matrixSequences;
 
-
     if (jalviewMatrix.width() != jalviewMatrix.height())
     {
       // some kind of warning?
     }
+    int i = 0;
+
+    for (Sequence sequence : sequences)
+    {
+      identifiers[i] = sequence.getName();
+      i++;
+    }
 
   }
 
@@ -48,6 +55,13 @@ public class ForesterMatrix implements DistanceMatrix
     {
       // some kind of warning?
     }
+    int i = 0;
+
+    for (String identifier : matrixIdentifiers)
+    {
+      identifiers[i] = identifier;
+      i++;
+    }
 
 
   }
@@ -55,14 +69,13 @@ public class ForesterMatrix implements DistanceMatrix
   @Override
   public String getIdentifier(int i)
   {
-    // TODO Auto-generated method stub
-    return null;
+    return identifiers[i];
   }
 
   @Override
   public int getIndex(String identifier)
   {
-    return 0;
+    return Arrays.asList(identifiers).indexOf(identifier);
   }
 
   /**
@@ -76,7 +89,7 @@ public class ForesterMatrix implements DistanceMatrix
 
   /**
    * See {@link MatrixI#getValue(int,int)} except that the order of column, row
-   * in the parameters is inverted here
+   * in the parameters is inverted here (as that is how forester demands it)
    */
   @Override
   public double getValue(int col, int row)
@@ -87,13 +100,13 @@ public class ForesterMatrix implements DistanceMatrix
   @Override
   public void setIdentifier(int i, String identifier)
   {
-    // TODO Auto-generated method stub
+    identifiers[i] = identifier;
 
   }
 
   /**
    * See {@link MatrixI#setValue()} except that the order of column, row in the
-   * parameters is inverted here
+   * parameters is inverted here (as that is how forester demands it)
    */
   @Override
   public void setValue(int col, int row, double distance)
-- 
1.7.10.2